The Serb, champion in Melbourne a record nine times, boarded an Emirates flight Sunday bound for Dubai following the virtual hearing that decided his fate.
A full court of three judges voted unanimously to uphold Minister of Health Alex Hawke's decision to cancel Djokovic's visa a second time.
After a 30-minute break to decide whether or not either party felt further orders were necessary, the court adjourned with no further orders incoming.
While the reasons for upholding the decision were not given by the judges at the virtual hearing, the Serb declined to speak as to present any new evidence.
What happened in federal court
The hearing, thrown together at the last minute so a ruling could occur before the tournament started, was to determine whether Hawke was being "unreasonable" in cancelling Djokovic's visa again.
Lawyers for the 34-year old put together a defense on the basis of three grounds, including the minister failing to properly consider the consequences of the latest visa cancellation.
Nick Wood, Djokovic's lead attorney, argued that the decision was "irrational" and that it could spark an uprising of rallies and protests among the anti-vaccine community.
Stephen Lloyd, representing Hawke, countered that under Australia's Migration Law, all the minister needed to was prove that the Serb "might" be a public health risk considering he is unvaccinated.
He added that Djokovic's anti-vaccine attitude was evident by his unwillingness to get the vaccinate despite having the opportunity to do so before arriving in Melbourne.
The final key point that Lloyd made was that the perception of Djokovic opposing vaccines was enough to incite protests among that community and that others would try to follow his lead in disregarding the rules.
Reaction to the decision
Following the ruling and just prior to his official deportation, Djokovic released a statement that read as follows:
"I would like to make a statement to address the outcome of today's Court hearing. I will now be taking some time to rest and recuperate, before making any further comments beyond this.
"I am extremely disappointed in the court's ruling to dismiss for judicial review of the Minister's decision to cancel my visa, which means I cannot stay in Australia and play the Australian Open.
"I respect the court's ruling and will cooperate with authorities in regards to my departure from the country.
"I am uncomfortable that the focus of the past few weeks has been on me and I hope that we can all now focus on the game and tournament that I love. I would like to wish the players, tournament officials, staff, volunteers and fans all the best for the tournament.
"Finally, I would like to thank my family, friends, team, supporters, fans and my fellow Serbians for your continued support. You have all been a great source of strength to me."
Chief judge James Allsop reacted the ruling came down to whether the minister's decision was "irrational or legally unreasonable."
Hawke reacted by stating "Australia's strong border protection policies have kept us safe during the pandemic, resulting in one of the lowest death rates, strongest economic recoveries, and highest vaccination rates in the world.
"Strong border protection policies are also fundamental to safeguarding Australia's social cohesion, which continues to strengthen despite the pandemic."
Prime Minister Scott Morrison also released statement, supporting both Hawke and the court's ruling.
"I welcome the decision to keep our borders strong and keep Australians safe. As I said on Friday, Australians have made many sacrifices during this pandemic, and they rightly expect the result of those sacrifices to be protected.
"Over the pandemic, together we achieved one of the lowest death rates, strongest economies and highest vaccinaton rates in the world. Strong borders are fundamental to the Australian way of life as is the rule of law.
"Our government has always understood this and has been prepared to take the decisions and actions necessary to protect the integrity of our borders.
"It is now time to get on with the Australian Open and get back to enjoying tennis over the summer."